CHAPTER 11.thechemicalmechanismsofmanycentralprocessesoflifearenowunderstoodCHAPTER 11.thechemicalmechanismsofmanycentralprocessesoflifearenowunderstoodofDNAdouble-helixstructure.*elucidationofflowofinformationfromgenetoprotein.*determinationof3D-structureandmechanismofactionofmanyproteinmolecules.*unravelingofcentralmetabolicpathways.*muchlearnedaboutmolecularmachinesthatharvestenergy,detectsignals,andprocessinformation.*developmentofDNAtechnologymonmolecularpatternsandprinciplesunderliethediverseexpressionsoflifethesameusesamebuildingblocks構建元件toconstructmacromolecules.flowofgeneticinformationfromDNAtoRNAtoprotein.ATP,theuniversalcurrencyofenergyisgeneratedinsimilarways.???3.biochemistryisprofoundlyinfluencingmedicine???elucidationofmolecularlesionscausingmanygeneticdiseases.discoveryandimplementationofeffectivetherapies.clinicaldiagnostics,DNAprobesintheprecisediagnosisofinheriteddisorders,infectiousdiseases,andcancers.valuableproteinsproducedbygeneticallyengineeredstrainsofbacteriacontainingbinantDNA,e.g.insulin,growthhormone,andstimulatorsofbloodcelldevelopment.rationaldesignofnewdrugs.designedchangesingeneticendowmentofplants(inagriculture).???4.therapiddevelopmentofpowerfulbiochemicalconceptsandtechniquesinrecentyearshasenabledinvestigatorstotacklesomeofthemostchallengingandfundamentalproblemsinbiologyandmedicine?Howdoesafertilizedeggbrain,andtheliver(分化)?giverisetocellsasdifferentasthoseinmuscle,the????Howdocellsfindeachother相互識別informingacomplexorgan?Howisthegrowthofcellscontrolled生長調控?Whatarethecausesofcancer?WhatisthemolecularbasisofmentaldisorderssuchasAlzheimer’sdisease阿爾茨海默病(早老性癡呆)andschizophrenia精神癥(早發性癡呆)?5Molecularmodelsdepict3-Dstructureinterplaybetweenthe3-Dstructureofbiomoleculesandtheirbiologicalfunction,threetypesofatomicmodelstodepictmoleculararchitecturespace-fillingmodels空間充滿模型ball-and-stickandskeletalmodelsparisonmodelsReversiblemolecularinteractionsaretheheartofthedanceoflife.Weak,noncovalentforcesplaykeyrolesin??faithfulreplicationofDNAfoldingofproteinsintointricate3-Dforms?detectionofsignalmoleculesthreefundamentalnoncovalentbondsare1electrostaticbonds2hydrogenbonds3Vander?detectionofsignalmoleculesthreefundamentalnoncovalentbondsare1electrostaticbonds2hydrogenbonds3VanderWallsbonds無共用電子對,無化學鍵形成)thebiologicallyimportantpropertiesofwaterareitspolarityandcohesiveness極性和粘性watersolvatespolarmoleculesandhenceweakensionicandhydrogenbonds?itgreatlyweakenselectrostaticforcesandhydrogenbondingbetweenpolarmoleculesbycompetingfortheirattractionexcellenceofwaterasasolventposesaproblem,foritalsoweakensinteractionsbetweenpolarmoleculesnonpolargroupstendtoassociateinwater??nonpolarmoleculesorgroupstendtoclustertogetherinwaterhydrophobicattractionsareamajordrivingforcein:???foldingofmacromoleculesbindingofsubstratestoenzymesformationofcellmembranes?thebasisofahydrophobicattractionisthisenhancedfreedomofreleasedwatermoleculesnonpolarsolutemoleculesaredriventogetherinwaternotprimarilybecausetheyhaveahighaffinityforeachotherbutbecausewaterbondsstronglytoitself?CHAPTER 2STRUCTUREANDFUNCTIONProteinsplaycrucialrolesinvirtuallyallbiologicalprocessesenzymaticcatalysts酶促反應的催化劑enzymesexhibitenormouscatalyticpower;severalthousandenzymescharacterized鑒定andmanyofthemcrystallized結晶;nearlyallknownenzymesareproteins,sotheyarecentralindeterminingthepatternofchemicaltransformationinbiologicalsystemstransportandstorage儲存和轉運(小和離子)specificproteinsaretransporters運載蛋白ofmanysmallmoleculesandions;e.g.hemoglobinmyoglobin,transferrin運鐵蛋白ferritin鐵蛋白coordinatedmotion協調運動proteinsarethemajorcomponentofmusclemechanicalsupport機械支撐hightensilestrength抗張強度ofskinandboneisduetothepresenceofcollagen膠原,afibrous纖維狀proteinimmuneprotection免疫保護Antibodies抗體arehighlyspecificproteinsthatrecognizeandcombinewith: bacteria,andcellsfromotherorganismsgenerationandtransmissionofnerveimpulses神經刺激的產生和傳遞theresponseofnervecellstospecificstimuliismediatedbyreceptorproteins,e.g.Rhodopsin視紫紅質controlofgrowthanddifferentiation生長和分化的調控controlledsequentialexpressionofgeneticinformationisessentialfortheorderlygrowthanddifferentiation,e.g.repressorprotein阻遏蛋白,growthfactorprotein,insulin.Proteinsserveinallcellsassensorsthatcontroltheflowofenergyandmatter.Severalkeypropertiesenableproteinstoparticipateinsuchawiderangeoffunctions1.Proteinsarelinearpolymersbuiltofmonomerunitscalledaminoacids.Proteinsaretheembodimentofthetransitionfromthe1.Proteinsarelinearpolymersbuiltofmonomerunitscalledaminoacids.Proteinsaretheembodimentofthetransitionfromtheone-dimensionalworldofsequencestothethree-dimensionalworldofmoleculescapableofdiverseactivities.體現了一維序列向(能執行多種生物學功能的)三結構的過渡awiderangeoffunctionalgroups.Alcohols,thiols巰基,thioethers硫酯,carboxylicacids,carboxamides羧酰胺teinscaninteractwithoneanotherandwithotherbiologicalmacromoleculestoformcomplexassemblies.Macromolecularmachines:accuratereplicationofDNA,thetransmissionofsignalswithincells,andmanyotheressentialprocesses.Someproteinsarequiterigid,whereasothersdisplaylimitedflexibility.Rigidones:asstructuralelementsinthecytoskeletonorinconnectivetissue.Partswithlimitedflexibility:ashinges鉸鏈區springs彈性區,andlevers杠桿.＆builtfromarepertoireof20AAasthebasicstructuralunitsofprotein,anα-AAconsistsofanaminogroup氨基,acarboxylgroup羧基ahydrogenatomandadistinctiveRgroupallofthe4groupsbondedtoanα-carbonatom.sonamedbecauseitisadjacenttothecarboxyl(acidic)groupanRgroupisreferredtoasasidechain側鏈AAinsolutionatneutralpHarepredominantlydipolarions偶極離子(orzwitterions兼性離子)inthedipolarformofAA,theaminogroupisprotonated(-NH3+)質子化andthecarboxylgroupisdissociated(-COO－)解離ofAAvarieswithpHonlyLAAareconstituentsofproteinstwentykindsofsidechainsvaryinginsize,shape,charge,hydrogen-bondingcapacity,andchemicalreactivityarecommonlyfoundinproteinstheremarkablerangeoffunctionsmediatedbyproteinsresultsfromthediversityandversatilityofthese20kindsofbuildingblocksthesimplestone:Gly(glycine)甘Rgroup:Hitisuniqueinbeingopticallyinactive唯一(不具有不對稱碳原子從而)不具光學活性的AAAla(alanine)comesnextRgroup:CH3(methylgroup甲基)Largerhydrocarbonsidechain(3and4Catoms):Val(valine)纈,Leu(leucine)亮,andIle(isoleucine)異亮.Thesesidechainsarehydrophobic疏水.The3-Dstructureofwatersolubleproteinsisstabilizedbythecomingtogetherofhydrophobicsidechainstoavoidcontactwithwater上述AA(的側鏈是疏水的因而)屬非極性AA(Gly除外,脂肪族中性AA),水溶性蛋白因這些疏水側鏈在一起(避免與水接觸)而使其三維結構保持穩定Pro(proline)晡differfromothersinthatitssidechainisbondedtoboththenitrogenandtheα-carbonatom其側鏈(除同α-碳原子外)還同(氨基)氮原子成鍵(形成吡咯環),因此,它只是α-AA(而不是真正意義上的α-AA)ThreeAAwitharomaticside:Phe(phenylalanine)苯丙,Tyr(tyrosine)withareactivehydroxylgroup,Trp(tryptophan)色具吲哚環PheandTrparehighlyhydrophobicCys(cysteine)andMet(methionine)甲硫(蛋)containsulfuratomintheirsidesulfur-containingsidechainsarehydrophobic疏水Thesulfydrylgroup巰基ofCysishighlyreactive.Cysplaysaspecialroleinshapingsomeproteinsbyformingdisulfidelinks二硫鍵Ser(serine)絲andThr(threonine)巰基ofCysishighlyreactive.Cysplaysaspecialroleinshapingsomeproteinsbyformingdisulfidelinks二硫鍵Ser(serine)絲andThr(threonine)containaliphatichydroxylgroups羥基morehydrophilicandreactive.ThrandIlecontaintwocentersofasymmetry蘇和異亮含兩個不對稱中心(allotherAA,inthebasicsetof20,exceptforGly,containasingleasymmetriccenter)Lys(lysine)andArg(arginine)withverypolarsidechains,whichrenderthemhighlyhydrophilic.TheyarepositivelychargedatneutralpH.His(histidine)canbeunchargedorpositivelycharged.Hisisoftenfoundintheactivesitesofenzymes,whereitsimidazole咪唑ringcanreadilyswitchbetweenthesestatestocatalyzethemakingandbreakingofbonds.His經常參與酶的活性中心的構成,它是唯一一個R基(咪唑基)pKa7AA.Asp(aspartate)andGlu(glutamate)withacidicsidechains.Gln(glutamine)谷天冬酰胺aretheunchargedderivativesofGluandAsp.SevenAAArg,Lys,His,Asp,Glu,CysandTyr)havereadilyionizablesidechains易離子化的側鏈按R基化學結構分類:按R基極性性質分類:bypeptidebonds肽鍵toformpolypeptidechainsInproteins,theα-carboxylgroupofoneAAisjoinedtotheα-aminogroupofanotherAAbyapeptidebond(oramidebond酰胺鍵)AAjoinedbypeptidebondsformapolypeptidechaininapolypeptideiscalledaresidue殘基Amino-terminalresiduewiththeα-aminogroup,carboxyl-terminalresiduewiththeα-carboxylgroupMainchain(orbackbone)(regularlyrepeatingpart)andsidechain(variablepart)Someproteinscontaindisulfidebonds.Theresultingdisulfideiscalledcystine.胱氨酸Intracellular胞內proteinslackdisulfidebonds,whereasextracellular胞外proteinsoftencontainseveral.從而胞內蛋白還原程度高nonsulfurcross-linksderivedfromLyssidechainsmayalsobepresentinsomeproteins(e.g.collagen).AAsequencesthatarespecifiedbygenesThedeterminationoftheAAsequenceofinsulin(1953)isalandmarkinbiochemistrybecauseitshowedforthefirsttimethataproteinhasapreciselydefinedAAsequence.ofproteinsaregeneticallydeterminedthesequenceofnucleotidesinDNA,themoleculeofheredity,specifiesacomplementarysequenceofnucleotidesinRNA,whichinturnspecifiestheAAsequenceofaproteinDNA中脫氧核苷酸序列→RNA中核苷酸序列→多肽鏈(蛋白)AA序列ofthe20AAisencodedbyoneormorespecificsequencesofthreenucleotidesproteinsinallorganismsaresynthesizedfromtheirconstituentAAbyacommonmechanismareimportantbecauseoftheknowledgeonthemareveryhelpfulandessentialinelucidatingitsmechanismofaction(e.g.thecatalyticmechanismofanenzyme)闡明蛋白功能(酶催化機制)ofrelationsbetweenAAsequencesand3-Dstructuresofproteinsareuncoveringtherulesthatgovernthefoldingofpolypeptidechains揭示多肽鏈折疊的規則,AA序中遺傳信息和(執行其生物學功能的)蛋白三維結構之間的geneticmessageinDNA→ofrelationsbetweenAAsequencesand3-Dstructuresofproteinsareuncoveringtherulesthatgovernthefoldingofpolypeptidechains揭示多肽鏈折疊的規則,AA序中遺傳信息和(執行其生物學功能的)蛋白三維結構之間的geneticmessageinDNA→AAsequence→3-Dstructurethatperformsaprotein’sbiologicalfunctionthesequencedeterminationispartofmolecularpathology.AlterationsinAAsequencecanproduceabnormalfunctionanddiseasee.g.sickle-cellanemiaAA序列的改變導致疾病:鐮狀細胞貧血病cysticfibrosis囊性纖維化thesequenceofaproteinrevealsmuchaboutitsevolutionaryhistory進化史proteinmodificationandcleavageconfernewcapabilitiesmanyofthesetof20AAcanbemodifiedaftersynthesisofapolypeptidechaintoenhanceitscapabilitiesN-terminalofmanyproteinsareacetylated乙?；?whichmakesthemmoreresistanttodegradation許多蛋白的N端被乙?；?從而具有較強的抗(被蛋白酶)降解能力Innewlysynthesizedcollagen膠原,manyprolineresidueshydroxyproline羥晡氨酸(stabilizethefiber)ehydroxylatedtoformVcdeficiencyinsufficienthydroxylationofcollagenscurvy壞血病VKdeficiencyinsufficientγ-carboxyglutamateγinprothrombin凝血素→hemorrhageAntibodiesacquirecarbohydrate糖unitsonspecificAsnresidues(makeaproteinmorehydrophilic親水)細胞的抗體需加入糖使得更親水aproteincanbemademorehydrophobicbytheadditionofaFA脂肪酸toanα-aminogrouporaCyssulfhydrylgroup蛋白加入脂肪酸后則更疏水manyhormones(e.g.epinephrine腎上腺素)altertheactivitiesofenzymesbystimulatingthephosphorylationofthehydroxylAA(SerandThr)andphosphothreoninearethemostubiquitousmodifiedAAinproteinsgrowthfactor(e.g.insulin)actbytriggeringthephosphorylation觸發磷酸化ofthehydroxylgroupofTyrresidues.ThephosphategroupsonthesethreemodifiedAAcanreadilyberemoved,enablingthemtoactasreversibleswitchesinregulatingcellularprocessesSomeoncogenesactbystimulatingexcessivephosphorylationofTyrresiduesonproteins(調控細胞分化的蛋白)manyproteinsarecleavedandtrimmedaftersynthesisdigestiveenzymes:inactiveprecursorsstoredsafelyinpancreas胰腺→releasedintointestine→activatedbypeptidebondcleavageinbloodclotting,solublefibrinogenisconvertedintoinsolublefibrin血纖peptidebondcleavagemanypolypeptidehormones(e.g.adrenocorti-cotropichormone促腎上腺皮質激素)arisefromthesplitting裂解ofasinglelargeprecursorprotein,amolecularcornucopia豐饒之角(寶庫)proteinsofpolioareproducedbycleavageofagiantpolyprotein脊髓灰質炎precursor巨多蛋白前體severalkeyproteinsofHIV-1arisebyspecificcleavageofalongprecursormodificationandcleavageasessentialfeaturesofproteinformationandfunction.Thesefinishingtouchesaccountformuchoftheversatility,precision,andeleganceofproteinactionfinishingtouchesaccountformuchoftheversatility,precision,andeleganceofproteinactionandregulation(蛋白樣性并且精確無誤)修飾和切割使得其功能和調控(方式)具有極其多thepeptideunitisrigidandplanar剛性和同一平面的characteristicofproteinsisthattheyhavewell-defined3-Dstructuresstretched-outorrandomlyarrangedpolypeptideisdevoidofbiologicalactivity散亂、隨機排列的蛋白不具生物學活性functionarisesfromconformation構象,whichis3-DarrangementofatomsinastructureAAsequencesareimportantbecausetheyspecifytheconformationofproteins氨基酸序列規定了蛋白構象polypeptidechainscanfoldintoregularstructuressuchastheαhelixTheαhelixisarodlikestructure.Thetightlycoiledpolypeptidemainchainformstheinnerpartoftherod,andthesidechainsextendoutwardinahelicalarrayitisstabilizedbyhydrogenbondsbetweentheNHandCOgroupsofthemainchain.Thus,allthemain-chainCOandNHgroupsarehydrogenbonded.3.6AAperturnofhelix(3.6×1.5?),soAAspaced3or4apartinthelinearsequencearespatiallyquiteclosetooneanotherinanαhelix.Incontrast,AA2apartaresituatedonoppositesidesofthehelixandareunlikelytomakecontact.Theαhelixfoundin proteinsisright-handedclockwise)右手螺旋Theαhelixcontentofproteinsrangeswidely0~100%)胰凝乳蛋白酶isvirtuallydevoidofit,about75%ofmyoglobin肌紅蛋白andhemoglobinisαhelicalsingle-strandedαhelicesareusuallyshort(lessthan45埃)However,twoormoreαhelicescanentwinetoformverystablestructures(morethan1000),calledαcoils卷曲螺旋,e.g.inmyosinandtropomyosin原肌球蛋白(inmuscle),fibrin(inbloodclots),keratin(inhair),filaments纖絲(incytoskeletonofcells)TheelucidationofthestructureoftheαhelixisalandmarkinmolecularbiologybecauseitdemonstratedthattheconformationofapolypeptidechaincanbepredictedifthepropertiesofitscomponentsarerigorouslyandpreciselyknownβpleatedsheetsarestabilizedbyhydrogenbondingbetweenβstrandsApolypeptidechaininaβpleatedsheet,calledaβstrand,isalmostfullyextended完全伸展.(axialdistancebetweenadjacentAA:3.5?inβpleatedsheet,1.5?inαhelix)AnotherdifferenceisthatitisstabilizedbyhydrogenbondsbetweenNHandCOgroupsindifferentpolypeptidestrands(chain)不同多肽股(鏈)之間的氫鍵polypeptidechainscanreversedirectionbymakinghairpinturnsmostproteinshavecompact,globularshapesowingtoreversalsinthedirectionoftheirpolypeptidechains.Manyofthesearecalledtheβturnβ轉角plishedbyacommonstructuralelementtheessenceofthishairpinturnisthattheCOgroupofresiduenofapolypeptideishydrogen-bondedtotheNHgroupofresiduen+3apolypeptidechaincanabruptlyreverseitsdirectionβturnoftenconnectantiparallelβstrands,hencetheirnamealsoknownasreverseturnsorhairpinbends發夾轉角膠原βturnoftenconnectantiparallelβstrands,hencetheirnamealsoknownasreverseturnsorhairpinbends發夾轉角膠原helixisstabili-zedbyprolineandhydroxyproline羥晡氨酸aspecialtypeofhelixispresentincollagen,themostabundantproteinofmammals.Itisthemainfibrouscomponentofskin,bone,tendon腱,cartilage軟骨,andteeth.膠原原纖是原膠原 285x103),由三股纏繞的多肽鏈(每股約1000維的基本結構)組成.itcontainsthreehelicalpolypeptidechains,eachnearly1000residueslongnearlyeverythirdresidueisGly(33%)Pro(13%)isalsopresenttoamuchgreaterextentCollagencontains4-hydroxyproline(Hyp,9%)(xPro,yHyp)ThesequenceGly-Pro-Hyprecursfrequentlycollagenisarod-shapedmolecule.Thehelicalmotifofitsthreechainsisentirelydifferentfromthatoftheαhelixhydrogenbondswithinastrandareabsent無鏈內氫鍵(因非常伸展)eachofthethreecollagenhelicesisstabilizedbystericrepulsion空間排斥ofthepyrrolidonerings吡咯環oftheProandHypresiduesthishelicalformismuchmoreopenthanthetightlycoiledαhelixthethreestrandswindaroundeachothertoformasuperhelicalcablethethreestrandsarehydrogenbondedtoeachother,theHdonorsaretheNHofGly,aretheCOof“x”residuesontheotherchains.ThehydroxylgroupsofHypresiduesalsoparticipateinhydrogenbondingtheonlyresiduethatcanfitinaninteriorpositionisGly三股螺旋中的每條鏈的第三個殘基面向或位于擁擠的中心軸處,唯一能適合此位置的殘基是甘氨酸proteinsarerichinhydrogen-bondingpotentiality潛能allreversiblemolecularinteractions(theforcesthatdeterminethe3-Darchitectureofproteins)inbiologicalsystemsaremediatedby(electrostaticbonds靜電鍵hydrogenbondsvanderWaalsbonds間如此,內部也是這樣)the20fundamentalAAalsocanparticipateinhydrogenbondingThesidechainsofTrpandArgcanserveashydrogenbonddonorsonlyLikethepeptideunititself,thesidechainsofAsn,Gln,Ser,andThrcanserveashydrogenbonddonorsandacceptorsThehydrogen-bondingcapabilitiesofLys(andterminalaminogroup),AspandGlu(andterminalcarboxylgroup),Tyr,andHisvarywithpH.Thehydrogen-bondingmodesoftheseionizableresiduesarepH-dependentwater-solubleproteinsfoldintocompactstructureswithnonpolarcoresMyoglobin肌紅蛋白myoglobinisanextremelycompactmolecule,whichisbuiltprimarilyofαhelix(eight).(singlepolypeptidechain,withheme血紅素protheticgroup)about70%ofthemainchainisfoldedintoαhelicesmuchoftherestofthechainformsturnsbetweenhelices4oftheturnscontainPro,whichtendstodisruptαhelicesbecauseofsterichindrance位byitsrigidfive-memberedring4oftheturnscontainPro,whichtendstodisruptαhelicesbecauseofsterichindrance位byitsrigidfive-memberedringthefoldingofthemainchainofmyoglobiniscomplexanddevoidofsymmetry不具對稱性Thestrikingfactisthattheinteriorconsistsalmostentirelyofnonpolarresidues(e.g.Leu,Val,Met,Phe)TheonlypolarresiduesinsidearetwoHis,whichplaycriticalrolesinthebindingofhemeoxygenItsoutsideconsistsofbothpolarandnonpolarresiduesThespace-fillingmodelalsoshowsthatthereisverylittleemptyspaceinsidethepolypeptidechainthereforefoldsspontaneouslysothatitshydrophobicsidechainsareburiedanditspolar,chargedchainsareonthesurfaceAAthispancreaticenzyme胰酶exemplifiesaratherdifferentmodeofproteinfoldingthissinglepolypeptidechainof124residuesisfoldedmainlyintoβstrandsitalsocontainsatightlypacked,highlynonpolarinterioritisfurtherstabilizedbyfourdisulfidebondintegralmembraneproteins整合性膜蛋白(膜內在蛋白)theyaredesigneddifferentlyfromproteinsthataresolubleinaqueoussolutionthepermeabilitybarrier滲透性屏障ofmembranesisformedbylipids,whicharehighlyhydrophobicthus,thepartofamembraneproteinthatspansthisregionmusthaveahydrophobicexteriorthetransmembraneportionofamembraneproteinusuallyconsistsofbundlesofαheliceswithnonpolarsidechainsfacingout膜蛋白的跨膜部分通常由α-螺旋(束)組成(非極性側鏈朝外)therearefourbasiclevelsofstructureinproteinarchitecturestructureistheAAsequencesecondarystructurereferstothespatialarrangementofAAresiduesthatarenearoneanotherinthelinearsequencesomeofthesestericrelationshipsareofaregularkind,givingrisetoaperiodicstructuretheαhelixandβstrandareelementsofsecondarystructuretertiarystructurereferstothespatialarrangementofAAresiduesthatarefarapartinthelinearsequence,andtothepatternofdisulfidebondsthedividinglinebetweensecondaryandtertiarystructureisamatteroftastequaternarystructurereferstothespatialarrangementofsubunitsandthenatureoftheircontactsonlyproteinscontainingmorethanonepolypeptidechainexhibitthislevelofstructuralorganizationhemoglobinconsistsoftwoαandtwoβchainsthesubunitinterfacesinthistetramer四聚體participateintransmittinginformationbetweendistantbindingsitesforO2,CO2,andH+esmakethemostofalimitedamountofgeneticinformationbyformingcoatsthatkindofsubunitrepetitivelyinasymmetricarray(如:60-聚對稱球狀體)supersecondarystructurereferstoclusters簇ofsecondarystructure.e.g.βαβunitDomain結構域:somepolypeptidechainsfoldintotwoor狀體)supersecondarystructurereferstoclusters簇ofsecondarystructure.e.g.βαβunitDomain結構域:somepolypeptidechainsfoldintotwoormorecompactregionsthatmaybejoinedbyaflexiblesegmentofpolypeptidechain,ratherlikepearlsonastring結構域:多肽鏈在二級結構或超二級結構的基礎上形成三級結構的局部折疊區,它是相對 的緊密球狀實體.對較小的球狀蛋白質 或亞基,結構域即三級結構(這些蛋白質或亞基是“單結構域”的);對較大的球狀蛋白質或亞基,其三級結構往往由兩個或多個結構域締合而成(它們是“多結構域”的)thesecompactglobularunitsarecalleddomainsinsizefromabout100to400AAresiduese.g.a25-kdLchainofanantibodyisfoldedintotwodomainsthesedomainsresembleeachotherwhichsuggeststhattheyarosebyduplicationofaprimordial原始geneanimportantprinciple:proteindomainsareoftenencodedbydistinctpartsofgenescalledexons一個外顯子編碼一個結構域ofaproteinspecifiesits3-Dstructure核糖核酸酶isasinglepolypeptidechainconsistingof124AAresiduesits4disulfidebondscanbecleavedreversiblybyreducingthemwithβ-mercaptoethanolβ-巰基乙醇ribonucleasecanbereducedbyβ-mercaptoethanolinurea尿素(8M)orguanidine胍基鹽酸intoarandom-coilconformationtheproductwasfullyreduced,randomlycoiledpolypeptidechaindevoidofenzymaticactivity,ordenaturedthedenaturedenzyme(freedofureaandβ-mercaptoethanolbydialysis透析)slowlyregainedtheenzymaticactivity(-SHoxidizedbyair)nearlyalltheoriginalenzymaticactivity(physicalandchemicalpropertiesoftherefoldedenzyme)wasregainedinformationneededtospecifythecomplex3-DstructureofribonucleaseiscontainedinitsAAsequence:sequencespecifiesconformationithadonly1%oftheenzymaticactivityofthenativeprotein(ifitwasreoxidizedin8Mureawhichwasthenremoved)thereasonisthatwrongdisulfidepairingswereformedwhenreducedribonucleasewasreoxidizedwhileitwasstillin8Murea(thendialyzedtoremove)thereducedmoleculewasreoxidizedthe“scrambled”ribonucleasespontaneouslyconvertedintofullyactive,nativeonewhentraceamountofβ-mercaptoethanolwereaddedtoanaqueoussolutionoftheproteinthisprocesswasdrivenentirelybythedecreaseinfreeenergyasthescrambledconformationswereconvertedintothestable,nativeconformationoftheenzymethenativeformofribonucleaseisthethermodynamicallymoststablestructurespecificbindingandtransmissionofstructuralchangesareattheheartofproteinactionthefirststepintheactionofaproteinisitsbindingofanothermoleculeproteinasaclassofmacromoleculesareuniqueinbeingabletorecognizeandinteractwithhighlydiversemoleculesmyoglobintightlybindsahemegroupwhenitspolypeptidechainispartlyfoldedtheacquisitionofhemeenablesmyoglobintocarryoutitsbiologicalfunction,whichistoreversiblybindO2proteinsalsocombinewithothermyoglobintightlybindsahemegroupwhenitspolypeptidechainispartlyfoldedtheacquisitionofhemeenablesmyoglobintocarryoutitsbiologicalfunction,whichistoreversiblybindO2proteinsalsocombinewithotherproteinstoproducehighlyorderedarrays(e.g.contractilefilamentsinmuscle)thebindingofforeignmoleculestoantibodyproteinsenablestheimmunesystemtodistinguishbetweenselfandnonselftheexpressionofmanygenesiscontrolledbythebindingofproteinsthatrecognizespecificDNAsequencesproteinsareabletointeractspecificallywithsuchawiderangeofmoleculesbecausetheyarehighlyproficientatformingcomplementarysurfacesandclefts(bytherichrepertoireofsidechains)thecatalyticpowerofproteinscomesfromtheircapacitytobindsubstratemoleculesinpreciseorientationandtostabilizetransitionstatesinthemakingandbreakingofbonds(e.g.carbonicanhydrase碳酸酐酶) 結合底物,精確(使不同底物靠近并采取最佳 ),穩定過渡態,然后形成新的(切斷原有的)化學鍵itbringssubstratesintocloseproximityandoptimizestheirorientationforreactionanotherrecurringcatalyticdeviceistheuseofchargedgroupstopolarizesubstratesandstabilizetransitionstatessomeproteinscontainmultiplebindingsitesthatcommunicatewitheachotheraconformationalchangeinducedbythebindingofamoleculetoonesiteinaproteincanalterothersitesthusproteinscanbebuilttoserveasmolecularswitchestoreceive,integrate,andtransmitsignals接受,整合和傳遞信號regulatorysitescalledallostericsitesthatcontroltheirbindingofothermoleculesandaltertheircatalyticrates(e.g.hemoglobin)allostericcontrolmediatedbyconformationalchangesinproteinmoleculesiscentraltotheregulationofmetabolisme.g.channelproteinsinthenervoussystema logicgates,akintoanANDgate“與”門onacomputechipproteinscontainingpairsofsitesthatarecoupledtoeachotherbyconformationalchangeshavethecapacitytoconvertenergyfromoneformtoanother(e.g.molecularmotorsinmusclecontraction)CHAPTER3EXPLORING PROTEINS??doAAsequencesspecifytheconformationsofproteins?Howdoproteinsbindspecificsubstratesandothermolecules,mediatecatalysis,andtransduceenergyandinformation?結合特異底物和其它,催化反應,轉換能量和信Anindispensablestepisthepurificationoftheproteinofinterest??????Anadageofbiochemistry: NeverwastepurethoughtsonanimpureproteinthethreekeyapproachestoanalyzingandpurifyingproteinsElectrophoresis電泳Chromatography層析Ultracentrifugation超離心automatedpeptidesequencingandtheapplicationofbinantDNAmethodsareawealthofAAsequencedataantibodiesarechoiceprobesforlocatingproteinsinvivoandmeasuringtheir?quantities蛋白內和定量測定?XandnuclearmagneticawealthofAAsequencedataantibodiesarechoiceprobesforlocatingproteinsinvivoandmeasuringtheir?quantities蛋白內和定量測定?Xandnuclearmagneticresonancespectroscopy核磁共振光譜學aretheprincipletechniquesforelucidating3-Dstructure,thekeydeterminantoffunction闡明決定蛋白功能的三維結構?Thesynthesisofpeptidesmakefeasiblethesynthesisofnewdrugs,functionalfragmentsofproteinsandTheProteomeistheFunctionalRepresentationoft表達ome蛋白質組(學)是組的功能▲Humangenome,all3billionbaseswith25000~30000genes▲Buttheknowledgeofgenomeisanalogoustoalistofpartsforacar—itdoesnotexplainhowthepartsworktogether▲Anewwordhasbeencoined,theproteome,tosignifyamorecomplexlevelofinformationcontent,theleveloffunctionalinformation,whichinteractionsofproteinsthatyieldafunctionalunit.(包括蛋白的類型,功能,功能▲thetermproteomeisderivedfromproteinsexpressedbyt▲Thegenometellsuswhatispossible什么是可能的,functionallypresent什么是(功能上)存在的passesthetype,functions,and間的相互作用)ome.theprote-ometellsuswhatis▲e.g.whichproteinsinteracttoformasignal-transductionpathwayoranionchannelinamem